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Solenoidal Model for Superstructure in Chromatin (Electron Microscopy/Packing Ratio/Supercoil) J Proc. Natl. Acad. Sci. USA Vol. 73, No. 6, pp. 1897-1901, June 1976 Biochemistry Solenoidal model for superstructure in chromatin (electron microscopy/packing ratio/supercoil) J. T. FINCH AND A. KLUG MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, England Communicated by F. H. C. Crick, March 18,1976 ABSTRACT Chromatin prepared by brief digestion of nu- matin and that nucleofilaments are normally organized in a clei with micrococcal nuclease, and extracted in 0.2 mM EDTA, higher level of folding. appears in the electron microscope as filaments of about 100 In this paper we present evidence obtained with the electron X diameter which coil loosely. In 0.2 mM Mg++ these "nucleo- filaments" condense into a supercoil or solenoidal structure of microscope for a state of chromatin in which nucleofilaments pitch about 110 A corresponding to the diameter of a nucleofi- are folded into supercoils or solenoidal structures of pitch about lament. It is proposed that the x-ray reflections at orders of 110 110 A. In our experiments we have used chromatin prepared A observed in chromatin originate in the spacing between turns by a brief micrococcal nuclease digestion of nuclei, which is of the solenoid rather than that between nucleosomes along the "native" in the sense that further nuclease digestion gives the nucleofflament. Ihe solenoidal structure appears to need histone same discrete pattern as does direct digestion of nuclei (15). HI for its stabilization. Under certain conditions, isolated nu- cleosomes can also aggregate into a similar structure. The sol- Chromatin prepared by methods that involve shearing does not enoidal structure can be correlated with the "thread" of diam- give such clear digestion patterns. In the presence of chelating eter about 300 A observed by other workers in nuclei. agents, this native chromatin appears as fairly uniform fila- ments of 100 A diameter, which are curly or loosely coiled. In The results of biochemical and other studies by various workers the presence of Mg++ ions, tightly coiled forms of the nucleo- (1-4) led Kornberg to propose a model for the basic structure filament are dominant, leading to a supercoil or solenoidal of chromatin (5). He suggested that it consists of a flexible chain structure in which the pitch corresponds to the diameter of a of repeating structural units of about 100 A diameter ("beads"), nucleofilament. each containing a stretch of DNA 200 base pairs long condensed around a protein core made out of eight histone molecules (two MATERIALS AND METHODS each of the four main types). These elementary units have been named "nucleosomes" (6). The physicochemical 'parameters Chromatin was prepared from rat liver nuclei after brief mi- for the model require that the nucleosomes are in close contact crococcal nuclease digestion, as described previously (15), to along the chain, and there is now good evidence from electron give an average length of about 40 nucleosomes, with a range microscopy that this is the case (7, 8). We call this close-packed roughly from 10 to 100. chain a "nucleofilament." A recent study by low angle x-ray Samples from dilute solutions of chromatin in appropriate scattering of dilute solutions of chromatin, prepared without media (e.g., 0.2 mM EDTA or 0.2 mM MgCl2) were applied to shearing, has given a mass per unit length consistent with nu- carbon-coated grids and washed with the same medium. At the cleosomes densely packed along the length of a nucleofilament typical chromatin concentrations used, a solution containing (9). 0.1 mM Mg++ is just sufficient to neutralize the phosphate Linear arrangements of beads in a partly extended form groups. For negative staining, the grids were then washed with ("beads-on-a-string") were first reported by Olins and Olins a few drops of 1% uranyl acetate, the excess being withdrawn (10) and Woodcock (11) in chromatin spilling out of nuclei lysed onto a filter paper. For shadowing of freeze-etched specimens, on the specimen grid, and made visible by negative or positive the specimens were fixed by floating the support grid on a drop staining. This extended form of chromatin probably results of 2% formaldehyde in the same solution for a few minutes and from the shearing forces present during the nuclear explosion. then were wasbed by floating on water. The specimens were A similar extended appearance is seen in the electron micro- then rapidly frozen in liquid nitrogen, dried on a Balzer's ap- graphs obtained by Oudet et al. from extracted chromatin, after paratus, and shadowed with platinum-carbon at an angle of 350, removal of histone HI (6). However, electron micrographs of as described by Nermut (16). small oligomers of beads prepared from nuclei by brief nuclease HI-depleted chromatin was prepared by treating chromatin digestion showed a preference for the nucleosomes to be in prepared as above with 0.45 M or 0.6 M NaCI, and dialyzing contact (8). against Tris buffer (5 mM Tris-acetate, 20 mM ammonium The nucleofilament can be correlated with the fairly uniform acetate, pH 6.8) after isolation on a sucrose gradient. Under fibers or threads of 100 A diameter seen in the electron mi- these conditions, virtually all the histone Hi was removed with croscope in chromatin specimens prepared by critical point almost no concomitant loss of the other four histones (L. Lutter, drying in the presence of chelating agents (4). However, spec- unpublished work). imens prepared in the absence of chelating agents show thicker fibers of about 250 A diameter (4, 12), suggesting that chro- RESULTS matin is normally present in a higher level of organization that breaks down when divalent ions are removed. The appearance Electron microscope observations of the thinner fibers has been attributed to the unwinding of Electron micrographs of chromatin in 0.2 mM EDTA or in 0.1 tertiary coiling (13, 14) or to the separation of two associated mM Mg++ are shown in Figs. 1 and 2. Chromatin appears as 100 A fibers (4, 14). Another line of reasoning, based on x-ray filaments about 100 A in diameter, which often tend to coil up studies and described below, also suggests that Kornberg's linear loosely. There is no visible repeat along the length of a filament. chain model only represents the first level of folding in chro- The filamentous character agrees with Sperling and Tardieu's 1897 Downloaded by guest on September 25, 2021 1898 Biochemistry: Finch and Klug Proc. Natl. Acad. Sci. USA 73 (1976) .s FIG. 2. Chromatin in 0.2 mM EDTA freeze etched and shad owed. The roughly parallel orientation of filaments probably arises during adsorption or washing of the specimen on the grid. X140,000. at least 300 'A thick, consistent with a helical character, rather than a two-dimensional zig-zag type of folding. FIG. 1. Electron micrographs of negatively stained chromatin The direction of the transverse striations in shadowed spec- prepared in (a) 0.2 mM EDTA, or (b) 0.1 mM Mg++. Arrows indicate imens does not consistently indicate a right- or left-handed helix, regions where loose coiling is evident. X140,000. although only one surface is being viewed. Since the slope of the helix is small, its left- or right-hand direction on one side of the fiber would be very susceptible to shear, and such shearing results on low angle x-ray scattering from dilute solutions of this is quite often present, as judged by the changes in obliquity of material in the same medium, which are consistent with the the striations seen in both types of specimens. Indeed, the scattering from a uniform cylinder of about 100 A in diameter variations in diameter and occasional pulled out fibers show that (9). the forces responsible for setting the relative phase of successive In a few instances (Fig. lb) the coiling of the nucleofilaments turns of the supercoil are not that strong or specific, at least for is so pronounced as to lead to a more condensed state, but the this type of preparation. Similarly, the helical parameters other majority of filaments are extended. In 0.2 mM MgCl2, however, than pitch are difficult to determine. The lack of visible detail almost all the material has this condensed character. The con- along the turns 'of the solenoids and the variation in diameter centration of Mg++ is not critical above 0.2 mM; similar results make it difficult to judge the number of nucleosomes per turn, are obtained up to 1 mM Mg++. In images of both negatively but the mean appears to be about 6 or 7. The variation in di- stained and shadowed specimens (Figs. 3 and 4) thick fibers or ameter may result from the relatively short length of the pieces elongated particles can be seen, of a diameter that is somewhat of chromatin used (about 40 nucleosomes), which correspond variable, even along the same fiber, but is usually in the range to only six turns of helix on the average. 300-500 A. In the negatively stained images striations can fairly This tendency for an association involving the "sides" of a often be seen running across the fibers, with a spacing of about nucleofilament is also shown, under certain circumstances, by 120-150 A. We regard the smaller values as the more signifi- individual nucleosomes. Aggregates with an appearance similar cant, since the longer spacings occur when the fibers are pulled to that of the Mg++-induced fibers have been obtained from out. The striations become increasingly difficult to detect as solutions of isolated nucleosomes (prepared as in ref. 17), which their spacing decreases, indicating the possibility of still tighter had been taken off a sucrose gradient and dialyzed against packing.
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